A shortage of big, fat worms called nightcrawlers—a popular bait with freshwater anglers in the U.S.—has pushed up prices nationwide and temporarily wiped out some merchants' stock at the height of the summer fishing season.

The culprit is bad weather in Ontario, the Canadian province where nightcrawlers are handpicked in the wild and shipped south by the millions. First, the long winter delayed picking from March to May. Then a dry...